{"id":"W4386830032","doi":"10.1101/2023.09.15.557936","title":"High-Throughput Short Sequence Typing Schemes for <i>Pseudomonas aeruginosa</i> and <i>Stenotrophomonas maltophilia</i> pure culture and environmental DNA","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Infections and bacterial resistance","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Polytechnique Montréal; Université de Montréal; Institut National de la Recherche Scientifique","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Aix-Marseille Université; California HIV/AIDS Research Program","keywords":"Stenotrophomonas maltophilia; Biology; Multilocus sequence typing; Typing; Pseudomonas aeruginosa; Computational biology; Genetics; Genotyping; In silico; Microbiology; Genome; Gene; Genotype; Bacteria","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002313505,0.0005412799,0.0004380322,0.00006544076,0.0003063235,0.0001856598,0.0002487163,0.0006899282,0.000003925067],"category_scores_gemma":[0.0000833732,0.0005600556,0.0001284372,0.0001037696,0.0002608475,0.00001874334,0.0006043396,0.0003338759,0.000004573789],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008297283,"about_ca_system_score_gemma":0.0001531051,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001819804,"about_ca_topic_score_gemma":0.000006688952,"domain_scores_codex":[0.9977195,0.00005126765,0.0003637304,0.00122136,0.0001572926,0.0004869059],"domain_scores_gemma":[0.9988067,0.00001892303,0.0001768888,0.0007021549,0.0001095599,0.0001857915],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00008011443,0.00004304065,0.002275141,0.0003040251,0.0001348446,0.00001303886,0.000004274497,0.000008899054,0.9964057,0.0002950366,0.0004267239,0.000009209691],"study_design_scores_gemma":[0.0006030912,0.0001903321,0.0109403,0.0002355117,0.0001449143,3.602899e-7,0.000008150502,0.00003738446,0.9106906,0.00001187837,0.07618841,0.000949047],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9929422,0.002594852,0.00124231,0.000127481,0.0009209179,0.0007994664,0.0012722,0.00009763391,0.000002961369],"genre_scores_gemma":[0.9883566,0.005355857,0.004694805,0.0001949162,0.0008756953,0.0003096146,0.00002263241,0.0001277798,0.00006202055],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08571503,"threshold_uncertainty_score":0.9996851,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01211741500798266,"score_gpt":0.2194109045843678,"score_spread":0.2072934895763852,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}